Investigation of Natural Dyes and Taxonomic Identification of Fibers Used in Chancay Textiles by Vibrational Spectroscopy and Mass Spectrometry.

Textiles provide a valuable source of information regarding past cultures and their artistic practices. Understanding ancient textiles requires identifying the raw materials used, since the origin of dyes and fibers may be from plants or animals, with the specific species used varying based on geography, trade routes and cultural significance. A selection of nine Chancay textile fragments attributed to 800-1200 CE were studied with liquid chromatography mass spectrometry (LC-MS) and direct analysis in real time mass spectrometry (DART-MS) to identify the chemical compounds in extracts of natural dyes used to create green, blue, red, yellow and black colors.

Development of a Combined Protein and Dye Extraction Approach for the Analysis of Keratin-Based Textiles.

Archaeological textiles represent precious remains from ancient culture; this is because of the historical and cultural importance of the information that can be obtained by such relics. However, the extremely complicated state of preservation of these textiles, which can be charred, partially or totally mineralized, with heavy soil or biological contamination, requires highly specialized and sensitive analytical tools to perform a comprehensive study. Starting from these considerations, the paper presents a combined workflow that provides the extraction of dyes and keratins and keratin-associated proteins in a single step, minimizing sampling while maximizing the amount of information gained.

Metabolomic profiling implicates mitochondrial and immune dysfunction in disease syndromes of the critically endangered black rhinoceros (Diceros bicornis).

The critically endangered black rhinoceros (Diceros bicornis; black rhino) experiences extinction threats from poaching in-situ. The ex-situ population, which serves as a genetic reservoir against impending extinction threats, experiences its own threats to survival related to several disease syndromes not typically observed among their wild counterparts. We performed an untargeted metabolomic analysis of serum from 30 ex-situ housed black rhinos (Eastern black rhino, EBR, n = 14 animals; Southern black rhino, SBR, n = 16 animals) and analyzed differences in metabolite profiles between subspecies, sex, and health status (healthy n = 13 vs.

Long-read HiFi sequencing correctly assembles repetitive silk genes in new moth and caddisfly genomes.

Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence.

Variation in Milk Proteins Across Lactation in and .

Milk is a critical nutrition source for all neonatal mammals. In addition to nutrition, milk contains a multitude of bioactive molecules that likely affect neonatal physiology, metabolism, and immune function. We suggest that changes in the milk proteome across lactation reflect the changing need of the neonate and juvenile offspring.

Deep Time Paleoproteomics: Looking Forward.

The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from and suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing.

We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called mandibulate archaic moths (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 Ma and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly contiguous genome with a contig N50 of nearly 17 Mb.

In-Line Dopant Generation for Atmospheric Pressure Ionization Mass Spectrometry.

A concentric trace gas permeation tube that diffuses chemical reagents to a central carrier gas stream is used to drive chemical reaction pathways and influence gas-phase chemistry for a variety of atmospheric pressure ionization sources for mass spectrometry. Tunable permeation through the reservoir-jacketed polymer membrane is triggered by the heated gas moving through the tube, evaporating the dopant into a sheath dry gas or into a sample stream in room air without diluting the analyte concentration. The permeator is used to add dopants to an electrospray plume for analyte ion charge reduction and to perform hydrogen-deuterium exchange on biomolecules in different spray conditions.

Mechano-chemical regulation of bat wing bones for flight.

Distal phalanges in bat wings have been hypothesized to be cartilaginous to allow for flight. We provide new evidence on how bat wing development might facilitate flight though protein-based regulation of bone mineralization and lead to more deflection at phalanx than humerus. Between Pteropus poliocephalus and Pteropus hypomelanus, two large bat species, we detected 112 proteins including 11 associated with mineralization and analyzed their distribution between the wing bones.

Creation of a peptide database of corneous beta-proteins of marine turtles for the identification of tortoiseshell: archaeological combs as case study.

Tortoiseshell is a proteinaceous material derived from the scutes of marine turtles, and was shaped into an abundance of objects, especially luxurious items, at its peak in the seventeenth and eighteenth century. It has continued to be used even after the advent of plastics and remains one of the main causes of illegal poaching of marine turtles, in particular the hawksbill turtle . Tortoiseshell is made of structural proteins, of which the most abundant are known as β-keratins, or 'corneous beta-proteins' (CBPs), a family of short proteins containing a central structure in β-sheets.

Proteomic profile of bone "collagen" extracted for stable isotopes: Implications for bulk and single amino acid analyses.

Rationale: Protein studies in archaeology and paleontology have been dominated by stable isotope studies to understand diet and trophic levels, but recent applications of proteomic techniques have resulted in a more complete understanding of protein diagenesis than stable isotopes alone. In stable isotope analyses, samples are retained or discarded based on their properties. Proteomics can directly determine what proteins are present within the sample and may be able to allow previously discarded samples to be analyzed.

Novel Proteomic Profiling of Epididymal Extracellular Vesicles in the Domestic Cat Reveals Proteins Related to Sequential Sperm Maturation with Differences Observed between Normospermic and Teratospermic Individuals.

Extracellular vesicles (EVs) secreted by the epididymal epithelium transfer to spermatozoa key proteins that are essential in promoting motility and subsequent fertilization success. Using the domestic cat model, the objectives were to (1) characterize and compare protein content of EVs between segments of the epididymis, and (2) compare EV protein compositions between normo- and teratospermic individuals (producing >60% of abnormal spermatozoa). Epididymal EVs from adult cats were isolated and assessed via liquid chromatography tandem MS.

Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics.

The term proteoform describes all combinations of change in a protein, as elucidated through intact mass proteomics. Paleoproteomic studies have begun using digestion-free and top-down techniques to access information from ancient and historical remains. However, to discuss protein changes that uniquely occur to archaeological and paleontological proteomes as the result of diagenesis (i.

Chemical effects of diceCT staining protocols on fluid-preserved avian specimens.

Diffusible iodine-based contrast-enhanced computed tomography (diceCT) techniques allow visualization of soft tissues of fluid-preserved specimens in three dimensions without dissection or histology. Two popular diceCT stains, iodine-potassium iodide (I2KI) dissolved in water and elemental iodine (I2) dissolved in 100% ethanol (EtOH), yield striking results. Despite the widespread use of these stains in clinical and biological fields, the molecular mechanisms that result in color change and radiopacity attributed to iodine staining are poorly understood.

Altered protein levels in bone marrow lesions of hip osteoarthritis: Analysis by proteomics and multiplex immunoassays.

Aim: To assess tissue level changes of proteome and cytokine profiles of subchondral bone in hip osteoarthritis (OA) affected by bone marrow lesions (BMLs). We compared significant protein level differences in osteoarthritic bone with BMLs to control bone without bone marrow lesions.

Methods: Subchondral bone biopsies were taken from femoral heads of end-stage osteoarthritis patients with (BML, n = 21) and without (CON, n = 9) BMLs.

Proteomic and direct analysis in real time mass spectrometry analysis of a Native American ceremonial hat.

Complementary mass spectrometry analyses were performed to study a broken ceremonial hat of the Tlingit in the collection of the Smithsonian Institution National Museum of Natural History. The hat base and an associated cylinder are carved from wood and show multiple signs of age and breakage, as well as remnants of animal materials used for construction, decoration, and repair. Samples of animal tissues embedded in and attached to the wood were prepared for liquid chromatography-tandem mass spectrometry (LC-MS/MS), which identified proteins from five clades native to the object's area of origin.

Microwave-assisted acid hydrolysis for whole-bone proteomics and paleoproteomics.

Rationale: Whole-bone proteomic analyses rely on lengthy sample preparation including demineralization and digestion to break bone down into peptides to recover using mass spectrometry. However, microwave-assisted acid hydrolysis, a technique used in proteomic analyses of other soft tissues and cells, will combine both demineralization and digestion and only take minutes.

Methods: To test microwave-assisted hydrolysis on whole moose bone, we microwaved five concentrations of acetic and formic acids (15%, 12.

Rapid Evaluation of the Debromination Mechanism of Eosin in Oil Paint by Direct Analysis in Real Time and Direct Infusion-Electrospray Ionization Mass Spectrometry.

Eosin is a synthetic organic colorant prone to fading under the influence of light. On the basis of the growing interest in the understanding of the discoloration mechanism of eosin-based lakes, this study compares the ability of two ultrafast and ultrasensitive mass spectrometry techniques to detect eosin derivatives in complex matrices, such as oil media without the use of conventional separation columns or additional sample preparation protocols. Direct analysis in real time mass spectrometry (DART-MS) and direct infusion electrospray ionization mass spectrometry (DI-ESI-MS) were used to characterize the degradation pathway of eosin in oil media.

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils.

Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed.

Human Bone Paleoproteomics Utilizing the Single-Pot, Solid-Phase-Enhanced Sample Preparation Method to Maximize Detected Proteins and Reduce Humics.

Sample preparation has become an important part of bone proteomics and paleoproteomics and remains one of the major challenges to maximizing the number of proteins characterized from bone extractions. Most paleoproteomic studies have relied on in-solution digestion with the inclusion of filter-aided sample preparation (FASP) as effective methods to detect the proteome. However, neither of these are optimal because few proteins have been detected utilizing only in-solution digestion and the molecular weight cutoff of FASP may miss remaining fragments of proteins in fossil bone.

Accumulation of carboxymethyl-lysine (CML) in human cortical bone.

Advanced glycation end-products (AGEs) are a category of post translational modification associated with the degradation of the structural properties of multiple different types of tissues. Typically, AGEs are the result of a series of post-translational modification reactions between sugars and proteins through a process known as non-enzymatic glycation (NEG). Increases in the rate of NEG of bone tissue are associated with type 2 diabetes and skeletal fragility.

A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics.

The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection.

Solid Digestion of Demineralized Bone as a Method To Access Potentially Insoluble Proteins and Post-Translational Modifications.

Bone proteomics is an expanding field for understanding protein changes associated with disease as well as characterizing and detecting proteins preserved in fossil bone. Most previous studies have utilized a protocol with demineralization and extraction approach to isolate and characterize proteins from bone. Through near-complete EDTA demineralization, followed by solid digestion of the remaining bone pseudomorph, a total of 92 protein accessions were detected from dog bone.

High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer.

The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale.

Identification and characterization of glycation adducts on osteocalcin.

Osteocalcin is an important extracellular matrix bone protein that contributes to the structural properties of bone through its interactions with hydroxyapatite mineral and with collagen I. This role may be affected by glycation, a labile modification the levels of which has been shown to correlate with bone fragility. Glycation starts with the spontaneous addition of a sugar onto a free amine group on a protein, forming an Amadori product, and then proceeds through several environment-dependent stages resulting in the formation of an advanced glycation end product.